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ngless-toolkit / ng-meta-profiler

Profiler for metagenomics based on NGLess
https://ngless.embl.de
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om-rgc module version mismatch #1

Closed unode closed 5 years ago

unode commented 5 years ago

In https://github.com/ngless-toolkit/ng-meta-profiler/blob/4b7b49aebb1f766274d2fbbf084852b34187193a/marine-profiler.ngl#L4 we refer om-rgc 0.9 but we only have om-rgc 0.0. Should we a) create the 0.9 module or instead b) downgrade the ngless script to 0.0.

Since we also have the ng-meta-profiler scripts on Zenodo, if we go for b) we will need to update those as well.

unode commented 5 years ago

To note that in ngless we currently have a 0.9 symlink but ngless fails with:

[Wed 29-05-2019 07:53:57]: Looking for module om-rgc at `./Modules/om-rgc.ngm/0.9/module.yaml` and did not find it.
[Wed 29-05-2019 07:53:57]: Looking for module om-rgc at `/opt/ngless/bin/../share/ngless/data/Modules/om-rgc.ngm/0.9/module.yaml` and did not find it.
[Wed 29-05-2019 07:53:57]: Looking for module om-rgc at `/root/.local/share/ngless/data/Modules/om-rgc.ngm/0.9/module.yaml` and did not
find it.
[Wed 29-05-2019 07:53:57]: Downloading https://ngless.embl.de/resources/Modules/om-rgc.ngm/0.9.tar.gz
Exiting after internal error. If you can reproduce this issue, please run your script with the --trace flag and report a bug at https://github.com/ngless-toolkit/ngless/issues
/root/.local/share/ngless/data/Modules/om-rgc.ngm/0.9/module.yaml: openBinaryFile: does not exist (No such file or directory)

because there is no 0.9 folder in the 0.9.tar.gz file.

unode commented 5 years ago

I'm fixing the 0.9.tar.gz to include the correct version in the folder name and module.yaml.

unode commented 5 years ago

Should be fixed now.